Metroid: Recondite
by Ceu Praca
Summary: Onboard the clandestine Bottle Ship, working separately from the Federation, a team of scientists began illegally experimenting with creating bioweapons. Unfortunately, animals were not the only things they experimented on: Samus discovers a biologically tampered human in the aftermath of the Bottle Ship's destruction. Rated T to be safe. There is NO romance in this story!
1. Disturbance

**Disclaimer:** _Metroid_ belongs to Retro Studios, Nintendo, and Dark Samus. If I tried claiming ownership I'd end up being thrown into a vat of Phazon, so...no, I don't own it. This disclaimer will only be posted here because I feel no need to keep repeating myself in every chapter.

**Overly long A/N: **This is a multi-chaptered _Metroid_ fanfiction that I wrote in my spare time; new chapters will be posted sporadically. Basically, an _Other_ _M_ fanfiction, however, I have removed all of the stupid fallacies like Samus' codependent behavior and whatnot. Read for yourself; I'm not defending the game, but don't judge my fanfic just because you hated the game. I don't like _Other M_ much myself; this is sort of a "fixing-fic." One thing: the only _Metroid_ games I have ever played are the_ Prime Trilogy_ and _Metroid: Other M._ Anything I know about the other games comes from the Wikitroid, so forgive me if there are random errors in continuity. And in this story, then basically, the _Prime Trilogy_ either doesn't exist or hasn't happened. Yes, I'm flipping the timeline slightly; this is fanfiction, so I'm allowed to do that. (It's probably a good thing I don't own the _Metroid_ franchise, haha) These chapters are pretty short because I am writing this in my spare time when I'm not working on my _Legend of Zelda: Dragon Series. _Read the summary if you want to know what _Recondite i_s about.

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**1: Disturbance**

_I don't remember my life, if I ever had one. I don't know who my parents were, where I was born, or where I was before coming here. I don't even know my name. I possess information on only two things: I belong to the Galactic Federation, and…oh, right, I don't belong to them anymore. Not technically, anyway. That girl-creature, the AI Unit, she killed them. She killed them all._

Green eyes flashed open at the sudden sound of energy blasts overhead. A man, human, almost invisible under the heavy layers of steel that kept him tightly encased, unable to move anything beyond his eyes. His gaze drifted upward to the metal bridge far above, where he saw faint flashes of orange light coupled with the angry roar of a Reo swarm; something had agitated the creatures. Grimly, he wondered if MB would kill whoever it was that had managed to invade the ship.

_MB. Not much of a designation; even the insignificant guardbots have a better title. Still, she is powerful, and has nearly complete command over the entire Bottle Ship. Funny, she hates me because I'm human, but won't kill me because I'm…well, one of them._

The weapons fire ended, and he heard running footsteps. Whoever had disturbed the hive had come out of it alive, apparently. It didn't matter much to him, contained far beneath the upper walkways. A small sigh escaped the steel prison, and those eyes closed as he counted slowly, forcing himself to return to his meditations; thinking about what could lie above would only make his current situation worse. He was going nowhere, sustained only by the needles in his arm that fed him a constant stream of nutrients.

_I never deserved this. Unlike Dragonfly, I always followed orders, always did what I was told to. Why torment me simply for following orders? MB, kill me now. Death would be far easier than just sitting here, doing nothing._


	2. Red

**2: Red**

_Time means nothing to me now. Days and weeks pass by the same way, there is nothing to mark the hours for me. An endless routine of waking up, staring, and falling asleep again. My mind keeps drifting to the Reo hive incident; I want to know what had happened. A few other times, there had been more weapons fire above, the snarls of more animals, more running footsteps, occasionally sounding as if there was more than one person up there. I haven't used my voice in a month, though, and when I opened my mouth to call out to whoever it was, only a hoarse croak was heard._

Red. Everything was glowing red. Alarms blared, and animals ran, sensing danger but unable to escape it. Green eyes opened again, and he watched, confused, as things began to shut down. There was a faint tingling sensation as the needles withdrew from his arm, and his eyes widened. He held his breath, unsure of what was happening, then his steel cage hissed open, and he fell to the ground.

_I…I'm free. Did MB do something? That alarm…Protocol Zero-Five has been initiated! The Bottle Ship is going to self destruct!_ Hands that hadn't moved in a month somehow found the strength to push against the floor, and his feet shifted as he struggled to his feet, staggering as he fought to stay upright.

The man wasn't sure how he was able to move after being confined for so long, but he bolted, instinctively heading for the single-passenger escape pods that he knew were in a nearby room.

He skidded to a stop in front of a panel, and typed in a sequence, his muscles tense as the overhead blared out that there was less than a minute before everything went boom. _MB better not have changed the codes…yes!_ He dashed through and opened the nearest pod, sliding in, sealing it, and hitting the launch button without bothering to strap himself in first.

The pod launched as the overhead counted to zero, and the coffin-sized vehicle shook violently enough to slam his head hard into the wall, causing his vision to blur, but in spite of the sudden pain in his skull, he was focused on one thing: he was _free_.

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**A/N: **I promise, this is the last chapter that really has anything to do with _Other M._ XD


	3. Man

**3: Man**

The gunship circled slowly until it was facing the destruction, and Samus Aran gazed at the debris with a mixture of satisfaction and sadness. She was glad that the Bottle Ship was gone, that there was no longer any danger of bioweapons being used by the Galactic Federation, but she also felt pain, knowing that it was the place where hundreds of people had died. The place where most of Platoon 07 had died.

She glanced back at the helmet, then down at her smoke-stained Zero Suit; Samus had put herself in an incredibly dangerous position in order to retrieve the item, and knew full well that she would have died had she not been able to reach her ship in time. It was foolish of her to have gone after Adam's helmet, but she knew that it contained his log entries, access codes, and classified documents, and thus held invaluable data.

The console beeped, alerting her to an unidentified object emitting faint bursts of energy that was floating on the edge of the cloud of debris. After a moment's hesitation, she cautiously directed her ship to pick it up, both curious and confused as to how anything could have survived the explosion intact.

She activated her armor and allowed the ship to bring it inside; a cocoon-shaped structure, seven feet in length and three feet in width, made entirely of metal with a small designation engraved on the side. EP-01. She recognized it: a single-passenger escape pod, the kind used by the Federation in all of their major space stations.

She used her helmet's interface to hack the locking mechanism, forcing the pod to give her access to its contents, and the surface slid open, revealing a bald human male, seemingly unconscious and completely naked.

Samus was bewildered; there had been no humans on the Bottle Ship other than her at the time the explosion was initiated. How had this man ended up here? She lifted him carefully out of the pod and propped him in one of the two passenger seats, scanning him quickly.

_Subject 80% human male, 10% Tiroc, 10% unrecorded genetic coding. No known records._

She froze, an unwelcome feeling of dread creeping up on her. Tiroc were a particularly vicious strain of Space Pirates from the galaxy's core. She knew that the Federation had experimented with the Zebesian Pirates, but had they really…used a _human_ for their studies? That went far beyond merely breaking protocol; it was completely barbaric, to treat a fellow human like nothing more than an animal! She hoped she was wrong, but her Scan Visor was telling her otherwise.

She did a quick visual inspection of the man; he bore no scars, but a designation was tattooed on his left wrist: _ZTA-06-Lupus_.

That further confirmed her suspicion that the man was a Federation experiment; the military organization had a tendency to use Latin words when they gave codenames to things. She did another examination, this time checking for any injuries, and found a bruise on the back of his head, but he was otherwise okay.

Samus opened a compartment in her ship and pulled out a blanket, draping it carefully over the man to allow him some decency, then withdrew, eyeing him warily. Human he may have been, but if this man had Tiroc DNA, then there was no telling what he might do.

For all she knew, he could be completely wild. She wouldn't restrain him, though, unless he attacked her first; if this man _had_ been an experiment, she wanted him to know that she would treat him as a human, not a test subject, and therefore, she refused to tie him up like an animal.

She set her ship on a course for a small, uninhabited forest world called Criden, where she had a hidden base. She wasn't about to bring the man back to the Federation, and she would rather keep him hidden until she found out more about him.

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**A/N: **Yes, I sympathize with Platoon 07; it's not _their_ fault that they had an idiot commanding them; I rather liked Anthony, Lyle, Maurice, and KG. James was creepy; I didn't mind his death at all, and I was _glad_ when Adam was finally jettisoned. In this story, the _sole_ reason that Samus recovered that stupid football helmet was because it has top secret intel on it, and she wanted to hack it to find out what she could.


	4. Lupus

**4: Lupus**

When the ship came out of Light Space and set down on the planet five hours later, the man was still unconscious, so Samus picked him up, careful to restrain her armor-enhanced strength so she wouldn't accidentally crush him. She then carried him out into the base, which was concealed within a cliff.

She'd built the place years ago as a safe house, knowing that, while she may have been arguably the most powerful individual in the galaxy, she still needed a place to stay, and she couldn't live on her gunship _all_ the time. It consisted of a small kitchen, bathroom, and living area, with a cot off to one side.

She laid the man on the cot, then stood a little distance away to wait. There was no way she was taking her armor off, not unless she was able to know for sure that he wouldn't strike at her.

After another hour of standing there motionlessly, her patience was rewarded; the man twitched, then let out a long, deep sigh, eyes flickering open. She tensed instinctively, but the man merely sighed again, his brow furrowing as he seemed to slowly become aware of his surroundings. He tilted his head and glanced down at himself, looking confused by the blanket that was draped over him, then his gaze found her.

A moment's pause, then the man bolted to his feet and slammed his back against the wall defensively, the blanket falling to the floor. He clenched his hands, his expression guarded, but he made no move to attack. Probably because she was eight feet tall and wearing armor, and he was stark naked with zero weapons whatsoever.

Samus kept her arm cannon lowered to her side, praying inwardly that the man wouldn't be totally feral. "Easy," she said soothingly, for an instant remembering when Madeline Bergman had been just as defensive. However, the director had been panicking, scared out of her wits. This man, on the other hand, seemed completely calm, though he eyed her with the wariness of an untamed beast. "I won't hurt you," she added. Even if he couldn't understand her, she hoped he got the meaning behind her words.

There was a split second of profound silence, then the man cocked his head, emerald green eyes focused on her visor, which she had deliberately dimmed into transparency. He licked his lips, opening his mouth slightly; she heard a hoarse whisper, then he coughed, shaking his head.

She frowned as he raised a slender hand and pressed long fingers against his mouth, still shaking his head slightly. He touched his throat, his eyes still focused on her, like he was trying to convey something. Then he opened his mouth again and cupped his hand, miming a drinking action.

Immediately, Samus understood. Using her HUD to keep a close eye on him, she moved to the kitchen area and filled a cup with water, going back to hold it out to him. He inched closer and reached out, taking the water carefully and returning to his position against the wall, drinking slowly with an expression of gratitude.

He acted like the water was a lifeline, savoring every swallow, and, when he was finished, he held the cup out, nodding slightly. She took it back and set it on a nearby table, watching as he knelt to pick up the fallen blanket, tying it around his waist.

"I'm sorry," he said softly, his voice sounding weak. "I…haven't spoken in…over a month. Throat dried up."

"Who are you?" Samus asked, getting more confidant that he wasn't going to snap and strike at her. He obviously wasn't feral.

"ZTA-Zero-Six-Lupus," the man responded promptly.

She scowled, confused. "Is that actually your name?"

He shrugged. "I know, the full designation is a bit of a mouthful. You can just call me Lupus."

"But you don't have a name."

'Lupus' grimaced. "If I ever had a name, I don't remember it. Mind if I ask who you are? And where I am?"

"My name is Samus Aran, and you're in a safe house of mine, but I can't tell you exactly where, for security reasons."

He chuckled. "I understand. That's some pretty slick armor you have. That cannon must be really powerful. You with the Federation?"

She was amazed; if he was a Bottle Ship experiment, he wasn't giving any outward indication of it. He acted like a perfectly normal human male. "No, I am an independent bounty hunter. Why were you in an escape pod?"

Lupus moved slowly until he was sitting on the cot, staring down at himself as if doing an assessment. "Bottle Ship was about to explode, and I'm too young to die."

She raised an eyebrow, surprised at how relaxed and open he was being. "How old are you?"

He grinned. "Twenty-six. How old are _you_?"

Samus smiled back. Whoever he really was, he seemed as innocent as a child. "Almost thirty-three. Mind if I ask why you aren't wearing anything?"

He looked sheepish. "I, uh…I'm wearing a blanket?"

She laughed in spite of herself. "Sorry, that doesn't count."

Lupus smirked, running his hand over his bald head, his gaze straying to the tattoo on his wrist. "It's kind of a long story, but the short version is that I ticked someone off, and they shaved me, stripped me naked, and locked me in a cage."

"That sounds like cruel and unusual punishment. What did you do?"

"I killed five of my handlers," he said simply.

"'Handlers?'" Samus echoed. He'd really ended the lives of five people? Why did he sound so casual about it?

"Y'know…the people who trained me. We were training one day, my main handler told me to disarm them, and I…well, I killed them. It was an accident, really. I didn't mean to kill them, it just…happened. I was following orders, and forgot to restrain my strength. But they didn't care, they just caged me. I've been locked up ever since; they said they were going to move me off of the Bottle Ship within the week, but MB took over a few days before the transfer was to take place. After she took over, she…well, she didn't like me because I was a human, so she just left me in the cage. Are you going to lock me up, too?"

She was stunned; he'd said everything with such innocence. Though he hadn't confirmed it directly, she was ninety percent certain that he was, indeed, a Galactic Federation bioweapon. Though, what military benefit could come from combining Tiroc DNA with that of a human, she couldn't figure out.

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**A/N: **Samus has a hidden base for plot convenience, actually; you don't want an unpredictable, Pirate-DNA-infused experiment loose onboard a cramped spaceship, so I gave Samus a military bunker. You'll notice by now that Samus doesn't really show as many internal thoughts as Lupus does. And these chapters *might* get progressively longer; I'm not sure.


	5. Stay

**5: Stay**

Lupus was staring at her with a childlike curiosity, and, even though he'd just admitted to killing five people, Samus knew she couldn't lock him up; he looked genuinely apologetic for what he had done, and, somehow, she believed that he was telling the truth, that it had been an accident. "No, I'm not going to imprison you. How did you get out of your cage?"

"Protocol Zero-Five was initiated, and I think that caused my cage to shut off, because it released me for no reason. Then I ran and grabbed an escape pod because I wasn't in the mood to blow up."

"Zero-Five?" she repeated.

He chuckled. "Oops, sorry. It's the Federation codename for the Bottle Ship's self-destruct. What are you going to do with me?"

Samus eyed him calculatingly. He was a Galactic Federation experiment, and if they found out about him, they would immediately demand to take him back. As far as they were concerned, he was nothing more than property to be used or abused as they saw fit. He was starting to look nervous, so she finally responded. "I think I might just keep you here for now. I think you're smart enough to figure out what would happen in the Federation knew that one of their projects had escaped the Bottle Ship."

He flinched visibly. "Yeah, I know. Keep me here? And do _what_ with me?"

She felt a twinge of sympathy for him; the man seemed to expect that everyone wanted nothing more than to use him for their own ends. "I will do nothing. You're a free man, Lupus. You are not my property, and I am not your superior. However, from what you've indicated, you have been a prisoner for quite some time. I can help you recuperate. At the very least, I can get you some clothes."

He looked genuinely surprised, and, slowly, his mouth twitched into a small smile. "Well, then…thank you, Aran."

"Just call me Samus, please. The only people who ever call me 'Aran' are people that I really dislike."

He nodded. "Alright, then…Samus."

She chuckled. "Do you think you can stay put, then, while I go find you some clothes?"

"As long as you don't try dressing me up in girl's clothes, then sure," he replied with a smirk.

She shook her head, not sure whether to be amused or annoyed by his boyish attitude, leaving him to go back to her ship. Hopefully he was honest enough that he really _would_ stay without getting himself into trouble. His earlier comment about 'forgetting to restrain his strength' concerned her.

Whatever the Federation did to him may have made him dangerous, and she was determined to find out how, exactly, his Tiroc DNA would affect his behavior.

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**A/N: **Whenever the Galactic Federation is mentioned in negative terms, it is actually referring to the clandestine group of scientists that built the Bottle Ship illegally, not the main Federation that Samus works for.


	6. Others

**6: Others**

_For the first time in my life, I'm…safe. I have never been truly able to let my guard down like this; even back when the Federation was still in control, I was in near-constant danger, always having to keep an eye out for anything that might hurt me. Here, though, there's this…Samus. Oddly enough, I think I can trust her. She sounds like a human female, but that armor looks like nothing I've ever seen before. I don't think it's a human design, but it doesn't resemble any of the alien concepts I've studied, either._

Lupus inspected the room; it was sparsely furnished, clearly the domain of someone who wasn't home all that much, and what furniture there was gave no indication as to the owner's identity. He knew what a bounty hunter was, but he didn't quite understand; they were supposed to be some sort of assassin, right? Killers for hire? If that was true, then why was Samus being so nice to him?

_I'm sure her arm cannon can do quite a bit of damage, and those spikes on her knees and elbows…I'm definitely going to try to stay on her good side. At least, I will until she proves to be less than trustworthy. I'm puzzled by how she knows of the Bottle Ship, though. Supposedly, its existence was kept completely secret._

He froze instinctively when the door opened and the tall, armored figure entered again, this time holding a small bundle. Lupus forced himself to calm down; he knew she wasn't going to hurt him right now, but he couldn't really help the fact that he was trained to treat everything like a threat.

"That took you half an hour," he commented mildly, focusing on the glowing, green visor. He'd noticed immediately that she could seemingly control its opacity to hide her face. Right now, it was solid, and he couldn't see her eyes at all anymore.

Samus held out the bundle to him. "I'm sorry, it took longer than I expected. If my calculations are correct, then these should fit you."

He took the clothes carefully, noticing a bit of blue vegetation stuck to the bottom of her left foot. T_here must be a forest outside, or at least grass of some sort._ "Thank you." He discarded the blanket and pulled on the dark blue bodysuit, looking down at it; whatever material it was hung loose and comfortably, but not loose enough to be a hindrance.

"Lupus, do you mind if I ask you something?"

He shrugged. "Go ahead." _Bottle Ship is gone now, so it's not like anyone will come after me for revealing secrets._

"What was your purpose? What did the Federation intend you to do?"

_Well, that's an easy one._ "I don't know, honestly," he answered. "They never told me. My records said that I was brought to the Bottle Ship as an infant, and I certainly don't remember ever not being in the place. I know I contain two different strains of DNA in addition to my human blood, and I know that I was trained in everything from martial arts to artillery. I can defuse bombs and perform surgery, but…I don't know why I exist."

The bounty hunter stood completely motionless, and Lupus started to feel uncomfortable, unsure of whether she was staring at him or not because of the opaque visor. _What? I told you the truth! Don't you believe me?_

"What does the 'ZTA' in your designation stand for?" she asked abruptly.

"I…I don't…they never told me. The meaning isn't in any of my records."

Another moment of silence, as though she was processing that, then, "Why are you listed as 'Zero-Six?'"

_Why is she asking so many questions?_ "Because I'm number six."

She took a step back from him. "You mean there were five more…like you?"

Lupus eyed her, frowning. "I'm not sure how much like me they were, exactly, but yes, there were five other human experiments. _DAJ-01-Dragonfly, DCH-02-Break, IJC-03-Albus, RHV-04-Ballistic, SNR-05-Pyrrus,_ and then there was me, _ZTA-06-Lupus_."

"That's odd; designations aren't normally that diverse from one another."

He shrugged. "I'm sure the GF had their reasons, but they never told us why we were each given the designations we were."

"So you knew the other five personally, then? What happened to them?"

He chuckled, shaking his head slightly and sitting down on the cot. "We would work in the same training center from time to time, but the Feds always took great pains to keep us from communicating with each other. Didn't want us conspiring together, I guess. The last of them was decommissioned two months ago."

"Decommissioned?" she repeated, her voice tinged with a note of harshness. "They weren't robots!"

"Try telling that to the Federation," he scoffed. "Each one apparently had some kind of 'flaw.' Dragonfly was too…headstrong, I think was the word they used. He had his own ideas and didn't like taking orders. Naturally, they didn't want a weapon with a strong tendency toward disobedience."

"And the other four?"

"Well, Albus was sort of…odd. Whatever DNA they gave him messed up his appearance quite a bit, and he had a lot of seizures. Break, on the other hand…he lived up to his name. He broke things. Things that he wasn't supposed to be breaking. Command got sick of how prone to violence he was. Ballistic, on the other hand, went crazy. Tried to shoot himself in the head, that failed, so he attacked Command. Pyrrus merely tried to blow up Sector 1; they found the bomb in time, but the fact that he even attempted it was enough to make them label him as a failure."

"In other words, they tampered with those men too much, and they snapped."

He nodded. "Yeah, pretty much."

"What did they do with the other five? Were they locked in cages like you were?"

"Maybe; I'm not sure. I think they were sent to the same place that the Federation had been about to send me. Some hidden base in one of the outlying systems."

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**A/N: **As you can tell by now, Lupus is the one with the internal thoughts that are _italicized_, whereas Samus' POV doesn't show internal thoughts at all. The splinter group evidently made two bases, the Bottle Ship and...something else. Samus' natural curiosity, the kind that drives her to investigate deaths and stop planetary warfare, will probably lead her to try locating this other base. Guess why the experiments were given the codenames that they were: _Dragonfly, Break, Albus, Ballistic, Phyrrus, Lupus._ Tell me the results of your guessing in a review. XD


	7. Info

**7: Info**

Samus absorbed all of the information quickly, unsure of what she was feeling at the moment; she had no reason to disbelieve Lupus, but he had just revealed the existence of a _second_ illegal base, and if the state the Bottle Ship had been in was any indication, there's no telling what could have happened in the other place.

"Do you know anything about this other base?" she eventually asked, frowning at him.

He looked vaguely annoyed. "I know it was codenamed _Refero_, and it was a place for the more…unique experiments. Humans, Metroids, Pirates, and the like."

From Lupus' point of view, her entire body went noticeably rigid, her arm canon abruptly glowing with a strange, white aura. "_Metroids_?" she hissed viciously. "Are you sure?"

He shrugged, eyeing her warily. "That's what I heard from Dragonfly, and one of the reasons he was decommissioned was because he'd hacked into the Bottle Ship's system and downloaded a lot of their files. You planning on shooting me or something?"

Samus made a concentrated effort to calm herself, the ice beam reabsorbing into her cannon. "Do you know where that base is located?"

Lupus sighed, rubbing the back of his neck with one hand. "No. Only the leader of the project would know where it is. If I did know where it was, I'd tell you. I have no love for the Federation; I'm not going to keep their secrets for them."

She felt uneasy, knowing that if there were really Metroids that had survived, the whole galaxy could be in danger again. "Lupus, I have to go. I need to find that base; you don't mind staying here, do you?"

He tipped his head to the side curiously, then stood up. "Why don't I help you? I'd get bored waiting here for you to come back, and trust me, it's _not_ pleasant when I have too much pent-up energy. I know more about the Bottle Ship and Refero than most, and I think I could be useful to you."

The huntress' first impulse was to say no, that she worked better alone, but then…if he came with her, there was a good chance they'd end up in combat at some point, and that might be a way for her to figure out just what the man was capable of. Maybe she'd even learn what his third slice of DNA was.

"Alright, you can come," she assented. "But you have to listen to me; I may not be in command of you, but if I tell you to do something, it will be to keep you alive."

He shrugged for the second time, smirking slightly. "Sure. Where do we go first?"

She wasn't sure whether or not she was making a mistake by bringing a genetically modified experiment with her, but nevertheless, Samus headed for the door, her HUD showing that Lupus was following quickly behind with long, even strides. "Planet Earth."

"Why there?" he asked, jogging briefly to catch up so that he was walking beside her on her left side; she deliberately shortened her strides so he could keep up without having to run.

"Because that's where the leader of the Bottle Ship project is," she answered slowly, the name echoing bitterly in her mind. "Raymond Elsin."

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So, was it really a good idea for Samus to bring a supposedly-super-powered human experiment with her? We'll see. This chapter was slightly shorter. Poor Samus; just when she thought she'd _finally_ exterminated the Metroids for good...this happens.


	8. Scan

**8: Scan**

Lupus' eyes lit up like a child in a toy factory when she brought him into her ship, and his hands visibly twitched before he folded his arms across his chest in a subtle effort to contain himself. Samus felt a flicker of amusement at his thinly veiled excitement, seating herself in the command chair and activating the ship's engines.

"Strap yourself in," she said, running a quick diagnostic before connecting her armor's systems directly into the mainframe. "You can look around once we're in light space."

He complied, smothering a grin. "Sorry, it's just…well, during training, the one thing I enjoyed more than anything was mechanics. Well, that and hand-to-hand combat. This is…it has to be the most advanced gunship I've ever even _heard_ of."

"It's the only one of its kind," she answered, piloting the vessel up, breaking atmosphere, and entering the proper coordinates. "Please don't meddle with anything, though."

"I won't," he responded as the ship entered light space. "Did you build it yourself?"

"Designed it, yes; building it required far more than what resources I had at the time."

He got up from the passenger seat and came to stand beside her chair, looking at the display reading interestedly. "How long will the transit be?"

She gestured to one screen, which was showing what appeared to be a countdown, only in a language that Lupus didn't recognize. "About seven standard hours and forty-nine minutes. I hope your patience level is high."

He chuckled, still studying things intently. "I spent a month immobilized in a cage; I'm used to waiting. Is your suit integrated into your skeletal system?"

She blinked in surprise, then glanced down at herself; it was easy to forget how utterly…_alien_ she could look while fully armored. She didn't blame him for thinking she was a cyborg. Still, as affable as Lupus was, she didn't trust him enough to take off her Varia Suit. "No," she eventually replied, choosing to keep it simple.

"Then how come you never take it off? Are you even human?"

"You have two separate kinds of DNA fused with your blood; are you?" she retorted. "Why I keep my armor activated is no concern of yours. But if you really must know, it is because I don't want you to try strangling me if I do take it off."

He held up both hands in a placating gesture. "Hey, easy, I was just curious. Don't worry, I'm not going to start trying to be best friends with you or anything. I get it, you don't trust me, and I don't trust you."

"As long as we understand each other then…" she muttered, frowning at him and doing another scan, wondering if she'd get more information now that he was awake.

_Subject: ZTA-06-Lupus, 80% human male, 10% Tiroc, 10% unrecorded genetic coding…searching for genome match…error: restart search process._

Samus was disappointed, but complied with her suit's directive. To her surprise, it gave an affirmative beep, more words displaying rapidly across her HUD, causing her to feel a rising sense of horror as she read the results.

_10% unrecorded genetic coding…searching for genome match…Subject displays similarity to Subject: [Fauna; Predator; Energy Class] Medusozoa Aevum Parisitus Tallonius: Common Name: Tallon Metroid._

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**A/N: **I'm just gonna let that last paragraph sink in for a bit. _Medusozoa Aevum Parisitus Tallonius_. English translation: Jellyfish Life Parasite Tallon. XD Yes, that Latin name for the Tallon Metroid is completely made up; I guess we know what Lupus' unrecorded 10% of DNA is now. I'm not a techno-minded person, so if her scan visor "sounds" funny, it's because I don't know computer codes, so I had no clue how to write the search results in a realistic fashion.


	9. Tiff

**9: Tiff**

"Metroid?" she hissed, rising and towering over him threateningly. "You have _Metroid_ DNA?"

Lupus gave her a dead stare for a moment, his face abruptly taking on a blank, unreadable expression, then he grimaced slightly. "And here I've been sort of hoping that your suit _didn't_ have some kind of scanning mechanism. I had a feeling you'd react badly to that."

"React badly?" Samus growled, her cannon beginning to glow with an ominous, white aura. "You're lucky I haven't shot you yet."

He rolled his eyes, seemingly unconcerned. "If you want to start a battle in a small area…well, I'll probably lose and you'll be fine, but I daresay your ship will be blasted full of holes. Not a good idea while we're in LS transit. Don't worry, I'm not going to start sucking anyone's energy or hovering randomly."

That gave her pause, and she grudgingly reabsorbed the beam. "You can do that?"

"_Maybe_. I'm neither confirming or denying; a little paranoia won't harm either of us."

"It might harm _you_," she muttered, glaring at him. "If you start floating, I _will_ shoot you."

Lupus merely stared at her, one corner of his mouth twitching slightly as if he was resisting the urge to smirk. "I will tell you one thing: I am very hard to kill. Nice side-effect of being part _Tallonius_."

"You probably have all the weaknesses of a Metroid, too," she pointed out. "I have been killing the things for a very long time now; I know how to take them down."

"I'm only _part_ parasite," he chuckled. "Let's just agree to not kill each other for now and try to get through this space trip alive, okay?"

Samus studied him carefully; at the very least, he didn't look like he had any means of siphoning energy. If he could do it, she'd expect him to have some kind of claws. Then again, to this day, no one knew exactly _how_ Metroids were capable of feeding the way they did.

"Agreed."

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**A/N: **I know, it's a horribly _stupid_ name for a chapter title; I couldn't think of anything else. I know this is short, but I've been trying to avoid the stereotypical "they went through hyperspace and I'm skipping over that because it's boring" thing. Although, in this fanfiction, hyperspace is referred to as "LS," or "Light Space." Oh, and guess what?! I have a picture of Lupus, for anyone who wants to know what he looks like. XD Now, FFN doesn't let you put links in stories, so just go to my profile; I'll have a link to the picture at the top there. :o)


	10. Clearance

**10: Clearance**

Samus always felt a bit pained whenever she had the need to return to Earth; not only was it where she'd made the decision to pretty much forsake anything to do with the Federation, it was the only planet where there were people who actually knew _her_, not just the living weapon that most thought she was.

Well, _person_, really. The other two were dead now. Not that it mattered; the point was, she hated making planetfall on Earth. It was a claustrophobic world, and she was already looking forward to _leaving_ before they'd even landed.

She and Lupus exited her gunship, and she locked it down, closing the blast shields for good measure. They may be the 'good guys,' but she didn't trust the Federation anymore; not after the whole Bottle Ship incident.

She noticed that her hybrid companion seemed tense as he walked beside her, his eyes scanning everything in view, and his expression became noticeably agitated when they approached the entrance to the Galactic Federation Headquarters. Following his gaze, she realized that it was the soldier guarding the entrance that he was focused on.

In spite of her wariness of any Metroid-ish tendencies he might have, Samus felt a bit of sympathy toward him. From his perspective, GF soldiers were nothing more than prison wardens. She held out her arm to halt him, turning to look down into his eyes. "Lupus, if you think you can't handle this, you can wait on the ship. I'm not asking you to come inside."

He frowned slightly, glancing at the soldier again before taking a deep breath. "I…I'm fine. Really, I am."

She wasn't all that convinced. "You won't snap and kill anyone?"

His lips twitched into a faint smirk before fading. "Don't worry, I won't bite."

She sighed. "You won't reveal who…or rather, _what_ you are?"

Lupus was silent for a moment, then shrugged. "I'll try. Walking around with _you_ doesn't help me keep a low profile at all, but I'll do my best."

"You have an odd sense of humor," she pointed out, although she knew he had a point: she wasn't exactly the most inconspicuous person to be traveling with.

"I've been locked in a cage for a long time; give me a break," he responded snarkily. "You don't have to worry, I'm not going to have a meltdown and destroy the base."

"Well, that's good," she replied, chuckling softly and resuming the walk toward the door.

"Please present verification," the guard said in a vaguely bored tone as they approached.

"Bounty Hunter Samus Aran, identity code one-three-five-seven-six," she answered, equally bored with the procedure, but, considering how many shapeshifters there were out there, she understood why it was necessary.

The soldier nodded and gave a casual salute, then consulted a PDA. "Of course. It'll take approximately two minutes to process."

She wasn't sure if she was imagining it or not, but he sounded slightly apologetic. She scanned him curiously. _Subject: Galactic Federation Marine NKE12, Private. Name: Tyler, J.O._ "That's fine; I'm used to it."

"Your friend needs to provide clearance as well."

"I can vouch for him."

The guard sighed almost inaudibly. "It's against regulations for anyone without clearance to be permitted entry. I'm sorry, but he'll have to wait outside."

She saw Lupus visibly stiffen and clench one fist, and she rolled her eyes, subtly phasing her gun so that it was strictly set to Wave Beam, just in case she ended up having to shoot the darn experiment. "Create clearance for him, Private Tyler. Please. I'm going to visit Colonel Elsin, and trust me, Elsin will _want_ to meet him."

Tyler seemed unimpressed. "Allowing an unregistered individual to meet with an official of this base is strictly prohibited. I could be discharged for breaking regs. Not gonna risk it."

"I'm not asking you to put anything on record," she answered, keeping her tone even and friendly. "Just let us walk past. Only Elsin will even know, and trust me, he won't give you a hard time when I'm done talking with him."

The soldier's PDA gave a soft beep, then there was a moment of silence as he processed her words, then he sighed again, opening the door for her. "Okay, okay. You and baldy can go in. Just…I'm warning you, Aran, if I lose my job, I'll steal a nuke and blast your ship."

"I'll consider myself warned."

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**A/N: **This is random, but the guy's normal name is Jack Owen Tyler.


	11. Meeting

**11: Meeting**

"You really could make him lose his job, you know," Lupus mused as they wove their way through the astonishingly uncrowded corridors within the base. "Not that I care too much, but you seem like the altruistic type, so that was kinda surprising."

"I am a bounty hunter, and I kill for a living. How is that altruistic?"

"Well, you saved my life, didn't you?"

"Mostly out of curiosity. I still don't trust you, and I'll kill you if you prove to be a threat."

He scowled slightly, then shrugged. "Fair enough. How'd you get tangled up in this whole Bottle Ship thing, anyway?"

"I intercepted a distress beacon, followed it, and ended up having to kill over seventy percent of the bioweapons onboard," she said flatly, entering a lift and selecting the top floor. "I trust that you will behave while I'm speaking with Elsin."

Lupus was silent a bit too long for Samus' liking, and she turned to frown at him, phasing her visor into transparency. He glanced at her, then nodded tightly. "Sure, I won't kill anyone."

The got out on Level Thirty, and soon reached a door guarded by two marines with a plaque reading _Colonel Elsin, R.C._

Samus looked at her companion one last time, still not convinced that he wouldn't do something stupid, then went up to the door. "I am here to see the Colonel," she addressed one of the guards.

The soldier had to tip his head back to see her visor. "I'm sorry, Miss Aran, he's busy right now."

"Is he in the middle of a meeting?" she asked politely.

"Uh…no, ma'am, he's filing reports and left orders that he was not to be disturbed."

"Tell him I'm here," she replied. "That I speak to him is a matter of importance."

The marine sighed, then gave a deferential nod. "One moment." There was silence, and she knew he was using his helmet communicator, then he shook his head. "The Colonel doesn't want to see you. His exact words were 'I don't care what it is, don't let her in.' I'm deeply sorry; he's not usually so rude."

Samus quelled the flash of anger that threatened to surface, and settled for merely closing her eyes briefly. "Ask him again."

"Ma'am, I don't think-"

"Ask him," she growled again, harsher this time. "Tell him that _Lupus_ has survived. He'll know what I mean."

The soldier hesitated, turning his helmet to look at his companion, who shrugged and didn't say anything. He eventually gave in. "All right, but if he says no again, you have to leave. Doesn't matter how famous you are, you can't just barge anywhere you want to go."

"If you insist," she muttered, annoyed.

"He says you can enter," the soldier spoke up, sounding nothing short of surprised. "But make it quick."

"Thank you." She made sure to close the door behind them.

Colonel Elsin was standing rigidly behind his desk, steely eyes narrowed into a glare, and Samus didn't miss that he had one hand holding a pistol.

"Aran, what is the meaning of this?" he snapped.

"You never cleaned up the loose ends of your little…project. Let's just say that I'm not happy that the Bottle Ship was experimenting on humans."

Elsin never took his eyes off Lupus, and, from scanning him, she deduced that he was both frightened and hostile. That last one was a no-brainer, but she didn't understand why he, of all people, would be scared.

"What do you want, Aran?" he finally growled. "You think threatening to frame me as part of the project will get you good standing with the Federation?"

"Pretending you aren't one of the ringleaders will get you nowhere," she responded. "I want you to give me the location of Refero Base."

He didn't say anything immediately, then slowly sat down, his pistol trained on Lupus. "Am I supposed to know what that is?"

"Don't play dumb," Lupus hissed, for the first time looking angry, stalking closer to the man. "The mere fact that you know _who_ and _what_ I am gives you away. You sent the others to Refero, and I want to know where it is."

Elsin's thumb flicked a switch on his weapon, turning the safety off, as the bioweapon pressed his palms flat to the surface of the desk and scowled down at him, giving Samus serious cause for concern as his skin began rippling with green energy.


End file.
